Graph based analysis for gene segment organization In a scrambled genome

•Scrambled gene segments from one gene can overlap or interleave with segments of another gene in Oxytricha trifallax.•Graph patterns can reveal patterns in inter-gene segment organization.•Graph properties can be represented as entries of vectors in higher dimensional space to form point cloud data.•Hierarchical clustering of the point cloud data is used to detect graph structures, and hence gene segment organization.•The analysis shows a single gene can interleave, or even contain all of the segments from fifteen or more other genes in between its segments.•Up to six genes can have their segments mutually interleaving or overlapping. DNA recombinant processes can involve gene segments that overlap or interleave with gene segments of another gene. Such gene segment appearances relative to each other are called here gene segment organization. We use graphs to represent the gene segment organization in a chromosome locus. Vertices of the graph represent contigs resulting after the recombination and the edges represent the gene segment organization prior to rearrangement. To each graph we associate a vector whose entries correspond to graph properties, and consider this vector as a point in a higher dimensional Euclidean space such that cluster formations and analysis can be performed with a hierarchical clustering method. The analysis is applied to a recently sequenced model organism Oxytricha trifallax, a species of ciliate with highly scrambled genome that undergoes massive rearrangement process after conjugation. The analysis shows some emerging star-like graph structures indicating that segments of a single gene can interleave, or even contain all of the segments from fifteen or more other genes in between its segments. We also observe that as many as six genes can have their segments mutually interleaving or overlapping.